HEADER CELL ADHESION 22-JAN-21 7BNG TITLE COMPLEX STRUCTURE OF SH3B DOMAIN WITH L-CANAVANINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOSTAPHIN; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.4.24.75; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS SIMULANS; SOURCE 3 ORGANISM_TAXID: 1286; SOURCE 4 GENE: HMPREF3215_01322; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: MAGIC KEYWDS CELL WALL TARGETING/BINDING, CWT, SH3, CELL ADHESION, COMPLEX, L- KEYWDS 2 CANAVANINE, STAPHYLOCOCCUS SIMULANS EXPDTA X-RAY DIFFRACTION AUTHOR P.H.MALECKI,I.SABALA REVDAT 3 31-JAN-24 7BNG 1 REMARK REVDAT 2 15-NOV-23 7BNG 1 ATOM REVDAT 1 17-FEB-21 7BNG 0 JRNL AUTH P.H.MALECKI,I.SABALA JRNL TITL COMPLEX STRUCTURE OF SH3B DOMAIN WITH L-CANAVANINE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 33216 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1063 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 36.8300 - 2.9400 0.98 4087 135 0.1607 0.1859 REMARK 3 2 2.9400 - 2.3300 0.99 4013 133 0.1573 0.1901 REMARK 3 3 2.3300 - 2.0400 1.00 4075 134 0.1338 0.1738 REMARK 3 4 2.0400 - 1.8500 1.00 4042 134 0.1320 0.2094 REMARK 3 5 1.8500 - 1.7200 0.98 4000 132 0.1534 0.2008 REMARK 3 6 1.7200 - 1.6200 0.99 3981 132 0.1802 0.2670 REMARK 3 7 1.6200 - 1.5300 0.99 3988 132 0.1976 0.2345 REMARK 3 8 1.5300 - 1.4700 0.97 3967 131 0.2501 0.3240 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7BNG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1292112723. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33240 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 36.833 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.732 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.74 REMARK 200 R MERGE FOR SHELL (I) : 1.18400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.590 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: 5LEO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M MES REMARK 280 MONOHYDRATE PH 6.5, 30% PEG 5K, COUNTER-DIFFUSION, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 27.61600 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 429 -41.75 80.57 REMARK 500 ASN B 429 -39.42 78.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GGB A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 501 DBREF1 7BNG A 398 493 UNP A0A133QQ41_STASI DBREF2 7BNG A A0A133QQ41 329 424 DBREF1 7BNG B 398 493 UNP A0A133QQ41_STASI DBREF2 7BNG B A0A133QQ41 329 424 SEQADV 7BNG SER A 398 UNP A0A133QQ4 THR 329 CONFLICT SEQADV 7BNG ALA A 400 UNP A0A133QQ4 SER 331 CONFLICT SEQADV 7BNG SER B 398 UNP A0A133QQ4 THR 329 CONFLICT SEQADV 7BNG ALA B 400 UNP A0A133QQ4 SER 331 CONFLICT SEQRES 1 A 96 SER ASN ALA THR TYR LYS VAL ASP GLY LYS GLY THR TYR SEQRES 2 A 96 TYR LYS ALA GLU SER ALA SER PHE THR ALA ASN TYR ASP SEQRES 3 A 96 ILE LYS THR ARG LEU ASN GLY PRO PHE ARG SER ASN PRO SEQRES 4 A 96 GLN SER GLY VAL LEU HIS PRO GLY GLN THR ILE LYS TYR SEQRES 5 A 96 ASP THR VAL MET LYS GLN ASP GLY HIS VAL TRP VAL VAL SEQRES 6 A 96 TYR THR GLY TYR SER GLY LYS ARG ILE TYR LEU PRO VAL SEQRES 7 A 96 ARG THR TRP ASP LYS ASN SER ASN THR LEU GLY PRO LEU SEQRES 8 A 96 TRP GLY ILE ILE ASN SEQRES 1 B 96 SER ASN ALA THR TYR LYS VAL ASP GLY LYS GLY THR TYR SEQRES 2 B 96 TYR LYS ALA GLU SER ALA SER PHE THR ALA ASN TYR ASP SEQRES 3 B 96 ILE LYS THR ARG LEU ASN GLY PRO PHE ARG SER ASN PRO SEQRES 4 B 96 GLN SER GLY VAL LEU HIS PRO GLY GLN THR ILE LYS TYR SEQRES 5 B 96 ASP THR VAL MET LYS GLN ASP GLY HIS VAL TRP VAL VAL SEQRES 6 B 96 TYR THR GLY TYR SER GLY LYS ARG ILE TYR LEU PRO VAL SEQRES 7 B 96 ARG THR TRP ASP LYS ASN SER ASN THR LEU GLY PRO LEU SEQRES 8 B 96 TRP GLY ILE ILE ASN HET GOL A 501 6 HET GGB A 502 12 HET GOL A 503 6 HET SO4 A 504 5 HET SO4 A 505 5 HET SO4 A 506 5 HET SO4 A 507 5 HET SO4 B 501 5 HETNAM GOL GLYCEROL HETNAM GGB L-CANAVANINE HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN GGB L-2-AMINO-4-(GUANIDINOOXY)BUTYRIC ACID FORMUL 3 GOL 2(C3 H8 O3) FORMUL 4 GGB C5 H12 N4 O3 FORMUL 6 SO4 5(O4 S 2-) FORMUL 11 HOH *225(H2 O) HELIX 1 AA1 SER A 398 TYR A 402 5 5 HELIX 2 AA2 SER B 398 TYR B 402 5 5 SHEET 1 AA1 6 LYS A 403 VAL A 404 0 SHEET 2 AA1 6 TYR A 410 ALA A 420 -1 O TYR A 411 N LYS A 403 SHEET 3 AA1 6 THR A 446 GLN A 455 -1 O VAL A 452 N LYS A 412 SHEET 4 AA1 6 HIS A 458 THR A 464 -1 O TRP A 460 N MET A 453 SHEET 5 AA1 6 ARG A 470 ASP A 479 -1 O LEU A 473 N VAL A 461 SHEET 6 AA1 6 THR A 484 LEU A 485 -1 O THR A 484 N ASP A 479 SHEET 1 AA2 7 GLN A 437 LEU A 441 0 SHEET 2 AA2 7 ILE A 424 LEU A 428 -1 N ILE A 424 O LEU A 441 SHEET 3 AA2 7 ARG A 470 ASP A 479 -1 O TYR A 472 N ARG A 427 SHEET 4 AA2 7 HIS A 458 THR A 464 -1 N VAL A 461 O LEU A 473 SHEET 5 AA2 7 THR A 446 GLN A 455 -1 N MET A 453 O TRP A 460 SHEET 6 AA2 7 TYR A 410 ALA A 420 -1 N LYS A 412 O VAL A 452 SHEET 7 AA2 7 GLY A 490 ASN A 493 -1 O ILE A 491 N THR A 419 SHEET 1 AA3 7 LYS B 403 VAL B 404 0 SHEET 2 AA3 7 TYR B 410 ALA B 420 -1 O TYR B 411 N LYS B 403 SHEET 3 AA3 7 THR B 446 GLN B 455 -1 O VAL B 452 N LYS B 412 SHEET 4 AA3 7 HIS B 458 THR B 464 -1 O TRP B 460 N MET B 453 SHEET 5 AA3 7 ARG B 470 THR B 477 -1 O VAL B 475 N VAL B 459 SHEET 6 AA3 7 ILE B 424 LEU B 428 -1 N ARG B 427 O TYR B 472 SHEET 7 AA3 7 GLN B 437 LEU B 441 -1 O LEU B 441 N ILE B 424 SHEET 1 AA4 3 LYS B 403 VAL B 404 0 SHEET 2 AA4 3 TYR B 410 ALA B 420 -1 O TYR B 411 N LYS B 403 SHEET 3 AA4 3 GLY B 490 ILE B 492 -1 O ILE B 491 N THR B 419 SITE 1 AC1 9 ILE A 424 LYS A 425 HOH A 607 HOH A 632 SITE 2 AC1 9 HOH A 634 HOH A 636 HOH A 647 TRP B 489 SITE 3 AC1 9 HOH B 624 SITE 1 AC2 7 ALA A 400 TYR A 402 LYS A 403 VAL A 404 SITE 2 AC2 7 HOH A 618 HOH A 629 HOH A 667 SITE 1 AC3 7 ARG A 433 HOH A 636 HOH A 654 TYR B 422 SITE 2 AC3 7 ASP B 423 ILE B 424 TRP B 489 SITE 1 AC4 5 SER A 398 ASN A 399 ALA A 400 HOH A 603 SITE 2 AC4 5 HOH A 655 SITE 1 AC5 8 SER A 398 TYR A 402 LYS A 454 ASN A 483 SITE 2 AC5 8 LEU A 485 HOH A 609 HOH A 660 HOH A 683 SITE 1 AC6 6 GLY A 465 TYR A 466 SER A 467 GLY A 468 SITE 2 AC6 6 LYS A 469 HOH A 628 SITE 1 AC7 2 ARG A 476 HOH A 621 SITE 1 AC8 6 SER B 398 TYR B 402 LYS B 454 ASN B 483 SITE 2 AC8 6 HOH B 608 HOH B 614 CRYST1 36.898 55.232 48.994 90.00 93.41 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.027102 0.000000 0.001613 0.00000 SCALE2 0.000000 0.018105 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020447 0.00000